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Identification of key genes related to seedlessness by genome-wide detection of structural variation and transcriptome analysis in 'Shijiwuhe' pear

文献类型： 外文期刊

作者： Liu, Yueyuan 1 ; Sun, Jieying 1 ; Zhang, Mingyue 1 ; Yang, Guangyan 1 ; Wang, Runze 1 ; Xu, Jintao 2 ; Li, Qingyu 3 ; Zha 1 ;

作者机构： 1.Nanjing Agr Univ, Ctr Pear Engn Technol Res, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Jiangsu, Peoples R China

2.Hebei Acad Agr & Forestry Sci, Changli Inst Pomol, Changli 066600, Hebei, Peoples R China

3.Yantai Acad Agr Sci, Yantai 264000, Shandong, Peoples R China

关键词： 'Shijiwuhe' pear; Seedlessness; Genomic structural variation; RNA-seq

期刊名称：GENE （ 影响因子：3.688； 五年影响因子：3.329 ）

ISSN： 0378-1119

年卷期： 2020 年 738 卷

页码：

收录情况： SCI

摘要： Seedless fruits are highly marketable because they are easier to eat than fruits with seeds. 'Shijiwuhe' is a seedless pear cultivar that is a mutant derived from an Fl hybridization population ('Bartlett' x 'Yali'). Little is known about the key genes controlling seedless pear fruit. In this study, field experiments revealed that seedless `Shijiwuhe' pear was not due to parthenocarpy, and that it was self-incompatible. Single nucleotide polymorphisms (SNPs), small insertions and deletions (InDels) and structural variations (SVs) were characterized using DNA sequencing data between `Shijiwuhe' and parental cultivars. A total of 1498 genes were found to be affected by SV and over 50% of SVs were located in promoter regions. Transcriptome analysis was conducted at three time points (4, 8, and 12 days after cross-pollination) during early fruit development of 'Shijiwuhe', 'Bartlett', and 'Yali'. In total, 1438 differentially expressed genes (DEGs) were found between 'Shijiwuhe' and parental cultivars 'Bartlett' and 'Yali'. We found 1193 SVs that caused differential expression of genes at 4 DACP. Among them, over 100 genes were in pathways related to seed nutrition and energy storage and 41 candidate genes encoded several important transcription factors, such as MYB, WRKY, NAC, and bHLH, which might play important roles in seed development. The qRT-PCR results also confirmed that the candidate genes with SVs showed differential expression between 'Shijiwuhe' pear and 'Bartlett' or 'Yali'. This study, which combined field experiments, SV detection, and transcriptome analysis might provide an effective way to predict the candidate genes regulating the seedless trait and important gene resources for genetic improvement of pear.

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